Semedo, 23, was arrested on Tuesday for his alleged involvement with others in holding a man who they threatened with a gun, according to media reports.
"The judge charged the footballer with crimes of attempted homicide, assault, threats, illegal detention, illicit possession of firearms and violent robbery," the Valencia court said in a statement on Thursday.
Semedo's agent, Catio Balde, told Portuguese television network TSF on Wednesday that his client had been tricked.
"Ruben was a victim of fraud, a large-scale swindle, probably of a financial nature. Against this situation he didn't react in the best possible way, but he was the victim. From what I've seen on Spanish television, it's a regrettable situation and not correct, but Ruben wasn't involved in this.
"The alleged kidnapping did not take place. It's a total lie that there was a kidnapping and torture. The gun didn't belong to Semedo even though they found it in his house," Balde said.
Villarreal said on its website that it would open an investigation into the player and take any necessary action.
Semedo joined the club last year from Sporting Lisbon for 14 million euros. He has made only three starts in La Liga this season due to a series of injuries.
(Reporting by Richard Martin in Barcelona and Rodrigo de Miguel in Madrid; Editing by Hugh Lawson)
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